GXYLT1

gene
On this page

Also known as FLJ43151

Summary

GXYLT1 (glucoside xylosyltransferase 1, HGNC:27482) is a protein-coding gene on chromosome 12q12, encoding Glucoside xylosyltransferase 1 (Q4G148). Glycosyltransferase which elongates the O-linked glucose attached to EGF-like repeats in the extracellular domain of Notch proteins by catalyzing the addition of xylose.

GXYLT1 is a xylosyltransferase (EC 2.4.2.-) that adds the first xylose to O-glucose-modified residues in the epidermal growth factor (EGF; MIM 131530) repeats of proteins such as NOTCH1 (MIM 190198) (Sethi et al., 2010 [PubMed 19940119]).

Source: NCBI Gene 283464 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 84 total
  • MANE Select transcript: NM_173601

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:27482
Approved symbolGXYLT1
Nameglucoside xylosyltransferase 1
Location12q12
Locus typegene with protein product
StatusApproved
AliasesFLJ43151
Ensembl geneENSG00000151233
Ensembl biotypeprotein_coding
OMIM613321
Entrez283464

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000280876, ENST00000398675, ENST00000905120, ENST00000905121

RefSeq mRNA: 2 — MANE Select: NM_173601 NM_001099650, NM_173601

CCDS: CCDS41771, CCDS41772

Canonical transcript exons

ENST00000398675 — 8 exons

ExonStartEnd
ENSE000009984264210581842106069
ENSE000010985134208184542087947
ENSE000010985144209791042098033
ENSE000010985154209744242097614
ENSE000012196724210956642109691
ENSE000012196804211900042119171
ENSE000012196994214442642144874
ENSE000015343004212975942129851

Expression profiles

Bgee: expression breadth ubiquitous, 236 present calls, max score 87.41.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.3444 / max 57.2026, expressed in 1672 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1304773.13281384
1304752.21161305

Top tissues by expression

253 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
pigmented layer of retinaUBERON:000178287.41gold quality
parietal pleuraUBERON:000240086.91gold quality
adrenal tissueUBERON:001830386.34gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.28gold quality
visceral pleuraUBERON:000240186.28gold quality
placentaUBERON:000198786.22gold quality
germinal epithelium of ovaryUBERON:000130484.45gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.44gold quality
epithelial cell of pancreasCL:000008383.97silver quality
thymusUBERON:000237083.72gold quality
palpebral conjunctivaUBERON:000181283.19gold quality
tibiaUBERON:000097982.92gold quality
calcaneal tendonUBERON:000370182.75gold quality
jejunal mucosaUBERON:000039982.65gold quality
islet of LangerhansUBERON:000000681.85gold quality
seminal vesicleUBERON:000099881.36gold quality
epithelium of nasopharynxUBERON:000195181.03gold quality
lower lobe of lungUBERON:000894980.64gold quality
monocyteCL:000057680.60gold quality
leukocyteCL:000073880.21gold quality
endometriumUBERON:000129580.09gold quality
ileal mucosaUBERON:000033179.69gold quality
stromal cell of endometriumCL:000225579.32gold quality
pericardiumUBERON:000240778.71gold quality
ganglionic eminenceUBERON:000402378.37gold quality
mucosa of sigmoid colonUBERON:000499378.37gold quality
embryoUBERON:000092278.36gold quality
epithelium of mammary glandUBERON:000324478.36gold quality
mammary ductUBERON:000176578.32gold quality
cartilage tissueUBERON:000241878.30gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no4.12

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

357 targeting GXYLT1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-5692A100.0074.406850
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-3646100.0073.565283
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-4682100.0068.891258
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-3163100.0077.238605
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4713-3P100.0065.92505
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-450099.9972.722367
HSA-MIR-366299.9973.825684
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-223-3P99.9970.141140
HSA-MIR-428299.9975.366408
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955

Literature-anchored findings (GeneRIF, showing 3)

  • We have identified two enzymes of the human glycosyltransferase 8 family, now named GXYLT1 and GXYLT2 (glucoside xylosyltransferase), as UDP-d-xylose:beta-d-glucoside alpha1,3-d-xylosyltransferases adding the first xylose. (PMID:19940119)
  • A stop-gain mutation in GXYLT1 promotes metastasis of colorectal cancer via the MAPK pathway. (PMID:35459861)
  • Exome Sequencing Implicates DGKZ , ESRRA , and GXYLT1 for Modulating Granuloma Formation in Crohn Disease. (PMID:37347142)

Cross-species orthologs

16 orthologs

OrganismSymbolGene ID
danio_reriogxylt1bENSDARG00000022550
danio_rerioENSDARG00000076111
mus_musculusGxylt1ENSMUSG00000036197
rattus_norvegicusGxylt1ENSRNOG00000005234
drosophila_melanogasterCG11149FBGN0031732
drosophila_melanogasterCG9171FBGN0031738
drosophila_melanogasterCG15483FBGN0032457
drosophila_melanogastershamsFBGN0039273
caenorhabditis_elegansbgnt-1.8WBGENE00008290
caenorhabditis_elegansWBGENE00009032
caenorhabditis_elegansbgnt-1.6WBGENE00010167
caenorhabditis_elegansWBGENE00010694
caenorhabditis_elegansWBGENE00010716
caenorhabditis_elegansbgnt-1.7WBGENE00011779
caenorhabditis_elegansWBGENE00015982
caenorhabditis_elegansWBGENE00017723

Paralogs (5): LARGE1 (ENSG00000133424), LARGE2 (ENSG00000165905), GXYLT2 (ENSG00000172986), XXYLT1 (ENSG00000173950), B4GAT1 (ENSG00000174684)

Protein

Protein identifiers

Glucoside xylosyltransferase 1Q4G148 (reviewed: Q4G148)

Alternative names: Glycosyltransferase 8 domain-containing protein 3

All UniProt accessions (1): Q4G148

UniProt curated annotations — full annotation on UniProt →

Function. Glycosyltransferase which elongates the O-linked glucose attached to EGF-like repeats in the extracellular domain of Notch proteins by catalyzing the addition of xylose.

Subcellular location. Membrane.

Similarity. Belongs to the glycosyltransferase 8 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q4G148-11yes
Q4G148-22

RefSeq proteins (2): NP_001093120, NP_775872* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002495Glyco_trans_8Family
IPR029044Nucleotide-diphossugar_transHomologous_superfamily
IPR051993Glycosyltransferase_8Family

Pfam: PF01501

Catalyzed reactions (Rhea), 1 shown:

  • 3-O-(beta-D-glucosyl)-L-seryl-[EGF-like domain protein] + UDP-alpha-D-xylose = 3-O-[alpha-D-xylosyl-(1->3)-beta-D-glucosyl]-L-seryl-[EGF-like domain protein] + UDP + H(+) (RHEA:56064)

UniProt features (9 total): glycosylation site 3, topological domain 2, chain 1, transmembrane region 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q4G148-F185.060.69

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (3): 173, 237, 278

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 219 (showing top): chr12q12, IWANAGA_E2F1_TARGETS_INDUCED_BY_SERUM, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, DODD_NASOPHARYNGEAL_CARCINOMA_UP, MILI_PSEUDOPODIA_CHEMOTAXIS_UP, GOBP_PROTEIN_O_LINKED_GLYCOSYLATION_VIA_N_ACETYL_GALACTOSAMINE, GOBP_PROTEIN_O_LINKED_GLYCOSYLATION, GOBP_GLYCOPROTEIN_METABOLIC_PROCESS, GOMF_GLYCOSYLTRANSFERASE_ACTIVITY, GOMF_UDP_GLYCOSYLTRANSFERASE_ACTIVITY, GOMF_PENTOSYLTRANSFERASE_ACTIVITY, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP, CHICAS_RB1_TARGETS_SENESCENT, JOHNSTONE_PARVB_TARGETS_2_DN

GO Biological Process (2): protein O-linked glycosylation via N-acetylgalactosamine (GO:0016266), protein O-linked glycosylation via glucose (GO:0180059)

GO Molecular Function (4): UDP-xylosyltransferase activity (GO:0035252), UDP-D-xylose:beta-D-glucoside alpha-1,3-D-xylosyltransferase activity (GO:0140563), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein O-linked glycosylation2
UDP-glycosyltransferase activity1
xylosyltransferase activity1
UDP-xylosyltransferase activity1
catalytic activity1
transferase activity1
cellular anatomical structure1

Protein interactions and networks

STRING

806 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GXYLT1UGGT1Q9NYU2895
GXYLT1F7P08709778
GXYLT1POGLUT1Q8NBL1725
GXYLT1POGLUT2Q6UW63628
GXYLT1NOTCH1P46531596
GXYLT1ZCRB1Q8TBF4583
GXYLT1POGLUT3Q7Z4H8575
GXYLT1POFUT1Q9H488566
GXYLT1ZNF782Q6ZMW2563
GXYLT1EGFP01133523
GXYLT1XXYLT1Q8NBI6511
GXYLT1EOGTQ5NDL2502
GXYLT1TMEM117Q9H0C3454
GXYLT1RBM46Q8TBY0437
GXYLT1XYLT1Q86Y38436

IntAct

34 interactions, top by confidence:

ABTypeScore
CHCHD4SSNA1psi-mi:“MI:0914”(association)0.640
GXYLT1CANXpsi-mi:“MI:0914”(association)0.640
CANXPGRMC1psi-mi:“MI:0914”(association)0.570
TOR1AIP1TXNpsi-mi:“MI:0914”(association)0.530
FBXO2TMEM131Lpsi-mi:“MI:0914”(association)0.530
ALKPIK3R2psi-mi:“MI:0914”(association)0.420
IGF1RHAX1psi-mi:“MI:0914”(association)0.350
INSRHAX1psi-mi:“MI:0914”(association)0.350
TYRO3HAX1psi-mi:“MI:0914”(association)0.350
PDGFRAGXYLT2psi-mi:“MI:0914”(association)0.350
SCGB2A2RTL8Cpsi-mi:“MI:0914”(association)0.350
GXYLT1P4HBpsi-mi:“MI:0914”(association)0.350
PCDHB3ESYT2psi-mi:“MI:0914”(association)0.350
TMEM106ATMEM131Lpsi-mi:“MI:0914”(association)0.350
PDGFRAQSOX1psi-mi:“MI:0914”(association)0.350
EPHA7PLOD2psi-mi:“MI:0914”(association)0.350
ALPPMAN2B1psi-mi:“MI:0914”(association)0.350
EFNA2MGST3psi-mi:“MI:0914”(association)0.350
GXYLT1CLGNpsi-mi:“MI:0914”(association)0.350
HTR1BSCAMP2psi-mi:“MI:0914”(association)0.350
AIFM1HSPA12Apsi-mi:“MI:0914”(association)0.350
CHCHD4PDHXpsi-mi:“MI:0914”(association)0.350
LCN6HIGD1Cpsi-mi:“MI:0914”(association)0.350
SLC30A10GOLIM4psi-mi:“MI:0914”(association)0.350
SLC39A11ESYT2psi-mi:“MI:0914”(association)0.350
SLC39A14ESYT2psi-mi:“MI:0914”(association)0.350
SLC39A7ESYT2psi-mi:“MI:0914”(association)0.350
SLC39A9TRAFD1psi-mi:“MI:0914”(association)0.350
FBXO11GXYLT1psi-mi:“MI:0915”(physical association)0.000

BioGRID (120): P4HB (Affinity Capture-MS), CANX (Affinity Capture-MS), P2RX2 (Affinity Capture-MS), OMA1 (Affinity Capture-MS), FKBP14 (Affinity Capture-MS), ASPHD2 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), VIM (Affinity Capture-MS), GXYLT1 (Affinity Capture-MS), GXYLT1 (Synthetic Lethality), GXYLT1 (Proximity Label-MS), GXYLT1 (Affinity Capture-MS), GXYLT1 (Reconstituted Complex), GXYLT1 (Proximity Label-MS), GXYLT1 (Proximity Label-MS)

ESM2 similar proteins: A0PJZ3, A2XFP3, A2XFT5, A2XFT6, B8AIZ4, C7J0P3, O04536, O48684, O88829, P08037, P15291, P15535, Q02527, Q09327, Q0V7R1, Q0WV13, Q10470, Q10MK2, Q10MQ0, Q16842, Q3UHH8, Q4G148, Q5CAZ6, Q5K027, Q5MJS3, Q5SP46, Q5ZKI6, Q68G12, Q6DE37, Q6GX83, Q6H765, Q6KB58, Q701R2, Q70D51, Q810K9, Q8CID3, Q8GWT1, Q8IXL6, Q8RXE1, Q92184

Diamond homologs: A0PJZ3, Q3UHH8, Q4G148, Q5SP46, Q5ZKI6, Q6DE37, Q6GX83, Q810K9, Q3U4G3

SIGNOR signaling

2 interactions.

AEffectBMechanism
GXYLT1up-regulatesNOTCH1glycosylation
GXYLT1up-regulatesNOTCH2binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 48 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO termPartnersFoldFDR
zinc ion transmembrane transport579.8×2e-06
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction610.7×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

84 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance49
Likely benign19
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1746 predictions. Top by Δscore:

VariantEffectΔscore
12:42097436:TCTTA:Tdonor_loss1.0000
12:42097437:CTTAC:Cdonor_loss1.0000
12:42097438:TTA:Tdonor_loss1.0000
12:42097439:TACAT:Tdonor_loss1.0000
12:42097440:A:ACdonor_gain1.0000
12:42097440:ACA:Adonor_loss1.0000
12:42097441:C:CAdonor_gain1.0000
12:42097441:CA:Cdonor_gain1.0000
12:42097441:CAT:Cdonor_gain1.0000
12:42097441:CATT:Cdonor_gain1.0000
12:42097441:CATTT:Cdonor_gain1.0000
12:42097587:C:Tacceptor_gain1.0000
12:42097587:CAT:Cacceptor_gain1.0000
12:42097589:T:TCacceptor_gain1.0000
12:42097593:C:CTacceptor_gain1.0000
12:42097595:C:CTacceptor_gain1.0000
12:42097596:G:Tacceptor_gain1.0000
12:42097611:CTTT:Cacceptor_gain1.0000
12:42097613:TT:Tacceptor_gain1.0000
12:42097615:C:CCacceptor_gain1.0000
12:42098029:TCATT:Tacceptor_gain1.0000
12:42098030:CATTC:Cacceptor_gain1.0000
12:42098034:C:CCacceptor_gain1.0000
12:42105814:TTACC:Tdonor_loss1.0000
12:42105815:TACCT:Tdonor_loss1.0000
12:42105816:AC:Adonor_gain1.0000
12:42105817:CC:Cdonor_gain1.0000
12:42105829:T:TAdonor_gain1.0000
12:42105962:T:Cacceptor_gain1.0000
12:42106066:TTAA:Tacceptor_gain1.0000

AlphaMissense

2893 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:42105869:G:CN271K1.000
12:42105869:G:TN271K1.000
12:42105905:A:CF259L1.000
12:42105905:A:TF259L1.000
12:42105907:A:GF259L1.000
12:42106026:T:AD219V1.000
12:42106026:T:GD219A1.000
12:42106032:T:AD217V1.000
12:42109599:A:CF193L1.000
12:42109599:A:TF193L1.000
12:42109600:A:CF193C1.000
12:42109601:A:GF193L1.000
12:42097503:C:AR367I0.999
12:42097503:C:GR367T0.999
12:42097509:C:TG365E0.999
12:42097513:G:CH364D0.999
12:42097565:A:CC346W0.999
12:42097566:C:GC346S0.999
12:42097567:A:TC346S0.999
12:42097583:A:CN340K0.999
12:42097583:A:TN340K0.999
12:42097932:A:CN322K0.999
12:42097932:A:TN322K0.999
12:42097939:A:GL320P0.999
12:42097942:T:AD319V0.999
12:42097942:T:GD319A0.999
12:42097943:C:GD319H0.999
12:42097944:T:AQ318H0.999
12:42097944:T:GQ318H0.999
12:42097948:T:AD317V0.999

dbSNP variants (sampled 300 via entrez): RS1000057471 (12:42125835 C>A,T), RS1000079230 (12:42119697 A>C), RS1000112666 (12:42098724 T>A,G), RS1000114745 (12:42131787 A>G), RS1000181488 (12:42140049 C>T), RS1000183005 (12:42090134 G>A), RS1000188262 (12:42146124 CAGAG>C,CAG), RS1000252466 (12:42132081 A>C,G), RS1000259356 (12:42111844 T>A,C), RS1000320371 (12:42120303 C>T), RS1000327793 (12:42096380 G>C), RS1000331806 (12:42111934 C>A), RS1000442396 (12:42096602 T>C), RS1000459380 (12:42135771 G>A,C), RS1000560306 (12:42094738 A>C)

Disease associations

OMIM: gene MIM:613321 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): primary amenorrhea (MONDO:1060208)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

7 associations (top):

StudyTraitp-value
GCST006585_2318Blood protein levels3.000000e-42
GCST007821_3Facial attractiveness (female raters)6.000000e-07
GCST008062_118Blood urea nitrogen levels2.000000e-08
GCST009325_101Parkinson’s disease or first degree relation to individual with Parkinson’s disease2.000000e-10
GCST009325_76Parkinson’s disease or first degree relation to individual with Parkinson’s disease7.000000e-12
GCST010002_215Refractive error3.000000e-11
GCST010774_11Essential hypertension (time to event)5.000000e-08

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0009892facial attractiveness measurement
EFO:0004918age at diagnosis

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

48 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
perfluorooctane sulfonic aciddecreases expression2
Air Pollutantsdecreases expression, increases abundance2
Formaldehydedecreases expression, increases expression2
Tetrachlorodibenzodioxindecreases expression2
aristolochic acid Idecreases expression1
dicrotophosdecreases expression1
2,4,6-tribromophenolincreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
bisphenol Aincreases expression1
decabromobiphenyl etherincreases expression1
2-butenaldecreases expression1
tetrabromobisphenol Aincreases expression1
perfluorooctanoic aciddecreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
pentabrominated diphenyl ether 100increases expression1
hexabrominated diphenyl ether 153increases expression1
bisphenol Saffects cotreatment, decreases expression1
jinfukangdecreases expression1
picoxystrobinincreases expression1
Resveratrolaffects cotreatment, increases expression1
Temozolomidedecreases expression1
Fulvestrantincreases methylation1
Vorinostatdecreases expression1
Leflunomidedecreases expression1
Acetaminophenincreases expression1
Benzo(a)pyreneincreases expression1
Cadmiumincreases expression1
Coalincreases abundance, decreases expression1

Clinical trials (associated diseases)

1 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT07164248Not specifiedCOMPLETEDEvaluation of Bone Mineral Density Indications and Outcomes in Female Adolescents: Implications for Early Detection of Osteopenia/Osteoporosis and Gynecologic Practice
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): essential hypertension, primary amenorrhea